Predicting permanent and transient protein-protein interfaces

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 5, 2013, Pages 805-818

  La, David ^a   Kong, Misun ^a   Hoffman, William ^a   Choi, Youn Im ^a   Kihara, Daisuke ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

Author keywords

Mutation pattern; Permanent and transient interactions; Phylogenetic substitution model; Protein binding interface; Protein protein interaction; Protein protein interaction network; Sequence analysis

Indexed keywords

AMINO ACID;

ACCURACY; AMINO ACID SUBSTITUTION; AREA UNDER THE CURVE; ARTICLE; BINDING AFFINITY; BINDING SITE; MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BINDING SITES; DATABASES, PROTEIN; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 84875868591     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24235     Document Type: Article

References (40)

1. Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AMJJ, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Sci 2011; 20: 482-491.
2. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000; 403: 623-627.
3. Ito T. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001; 98: 4569-4574.
4. Giot L. A protein interaction map of Drosophila melanogaster. Science 2003; 302: 1727-1736.
5. Xu Q, Canutescu AA, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL, Jr. Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol 2008; 381: 487-507.
6. Herberg FW, Dostmann WR, Zorn M, Davis SJ, Taylor SS. Crosstalk between domains in the regulatory subunit of cAMP-dependent protein kinase: influence of amino terminus on cAMP binding and holoenzyme formation. Biochemistry 1994; 33: 7485-7494.
7. Gegner JA, Dahlquist FW. Signal transduction in bacteria: CheW forms a reversible complex with the protein kinase CheA. Proc Natl Acad Sci USA 1991; 88: 750-754.
8. Lambright DG, Sondek J, Bohm A, Skiba NP, Hamm HE, Sigler PB. The 2.0 Å crystal structure of a heterotrimeric G protein. Nature 1996; 379: 311-319.
9. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res 2009; 38 (Database): D211-D222.
10. Krause R, Mering von C, Bork P, Dandekar T. Shared components of protein complexes-versatile building blocks or biochemical artefacts? Bioessays 2004; 26: 1333-1343.
11. Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004; 430: 88-93.
12. Fierens K, Gils A, Sansen S, Brijs K, Courtin CM, Declerck PJ, De Ranter CJ, Gebruers K, Rabijns A, Robben J, Campenhout S, Volckaert G, Delcour JA. His374 of wheat endoxylanase inhibitor TAXI-I stabilizes complex formation with glycoside hydrolase family 11 endoxylanases. FEBS J 2005; 272: 5872-5882.
13. Stratikos E, Gettins PG. Major proteinase movement upon stable serpin-proteinase complex formation. Proc Natl Acad Sci USA 1997; 94: 453-458.
14. Olson MW, Gervasi DC, Mobashery S, Fridman R. Kinetic analysis of the binding of human matrix metalloproteinase-2 and -9 to tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2. J Biol Chem 1997; 272: 29975-29983.
15. Kiel C, Selzer T, Shaul Y, Schreiber G, Herrmann C. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc Natl Acad Sci USA 2004; 101: 9223-9228.
16. van der Merwe PA, Barclay AN, Mason DW, Davies EA, Morgan BP, Tone M, Krishnam AK, Ianelli C, Davis SJ. Human cell-adhesion molecule CD2 binds CD58 (LFA-3) with a very low affinity and an extremely fast dissociation rate but does not bind CD48 or CD59. Biochemistry 1994; 33: 10149-10160.
17. Maenaka K, van der Merwe PA, Stuart DI, Jones EY, Sondermann P. The human low affinity Fcgamma receptors IIa, IIb, and III bind IgG with fast kinetics and distinct thermodynamic properties. J Biol Chem 2001; 276: 44898-44904.
18. La D, Kihara D. A novel method for protein-protein interaction site prediction using phylogenetic substitution models. Proteins 2012; 80: 126-141.
19. Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C. Transient protein-protein interactions: structural, functional, and network properties. Structure 2010; 18: 1233-1243.
20. Nooren IMA. New EMBO member's review: diversity of protein-protein interactions. EMBO J 2003; 22: 3486-3492.
21. Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Briefings Bioinform 2008; 10: 233-246.
22. Mintseris J. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 2005; 102: 10930-10935.
23. Ansari S, Helms V. Statistical analysis of predominantly transient protein-protein interfaces. Proteins 2005; 61: 344-355.
24. Block P, Paern J, Hüllermeier E, Sanschagrin P, Sotriffer CA, Klebe G. Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins 2006; 65: 607-622.
25. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 2004; 13: 190-202.
26. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003; 53: 629-639.
27. Liu R, Jiang W, Zhou Y. Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids 2009; 38: 263-270.
28. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004; 338: 181-199.
29. Chen H, Zhou H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005; 61: 21-35.
30. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996; 93: 13-20.
31. Nooren IMA, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003; 325: 991-1018.
32. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000; 28: 235-242.
33. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32: 1792-1797.
34. Miller S, Janin J, Lesk AM, Chothia C. Interior and surface of monomeric proteins. J Mol Biol 1987; 196: 641-656.
35. Jones D, Taylor W, Thornton J. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8: 275-282.
36. Henikoff S, Henikoff J. Amino acid substitution matrices from protein blocks. Proc Natal Acad Sci USA 1992; 89: 10915-10919.
37. Hosmer DW, Lemeshow S. Applied logistic regression. Hoboken, NJ: Wiley-Interscience; 2000.
38. Hilbe J. Logistic regression models. Boca Raton, FL: Chapman and Hall/CRC; 2009.
39. Gribskov M, Robinson NL. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996; 20: 25-33.
40. Tseng YY. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach. Mol Biol Evol 2005; 23: 421-436.